Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019453.1 Corchorus olitorius cultivar O-4 contig19486, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12709
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Found at i:452 original size:16 final size:16
Alignment explanation
Indices: 431--461 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
421 TAGATATTTG
431 ATAGTTGGAGTACTTC
1 ATAGTTGGAGTACTTC
*
447 ATAGTTGTAGTACTT
1 ATAGTTGGAGTACTT
462 ATTTATATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (16 bp):
ATAGTTGGAGTACTTC
Found at i:3565 original size:43 final size:43
Alignment explanation
Indices: 3504--3588 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
3494 TTTTTCACGT
3504 TTGAATTTCATTTCATTAAGGGAATGTTATAGATGAAGACAAG
1 TTGAATTTCATTTCATTAAGGGAATGTTATAGATGAAGACAAG
*
3547 TTGAATTTCATTTCATTAAGGGAATGTTATCGATGAAGACAA
1 TTGAATTTCATTTCATTAAGGGAATGTTATAGATGAAGACAA
3589 TTTGGTATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.35
Consensus pattern (43 bp):
TTGAATTTCATTTCATTAAGGGAATGTTATAGATGAAGACAAG
Found at i:3904 original size:31 final size:31
Alignment explanation
Indices: 3863--4009 Score: 154
Period size: 31 Copynumber: 4.7 Consensus size: 31
3853 GACGTGGCTT
* *
3863 GCCACATGTACCAAAAAGCAACATGTAGCAC
1 GCCACGTGTACCAAAAAGCGACATGTAGCAC
3894 GCCACGTGTACCAAAAAGCGACATG-AGGCAC
1 GCCACGTGTACCAAAAAGCGACATGTA-GCAC
* *
3925 GCCACGTGTACCAAAAAGTGACATGTATCAC
1 GCCACGTGTACCAAAAAGCGACATGTAGCAC
* * * *
3956 GCCATGTGTAACC-AAAAGTGACATGTGGCAT
1 GCCACGTGT-ACCAAAAAGCGACATGTAGCAC
* ** *
3987 GCCATGTGTTTCAAAAAGTGACA
1 GCCACGTGTACCAAAAAGCGACA
4010 CATGGCATGC
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
30 2 0.02
31 96 0.94
32 4 0.04
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (31 bp):
GCCACGTGTACCAAAAAGCGACATGTAGCAC
Found at i:3965 original size:62 final size:62
Alignment explanation
Indices: 3863--4009 Score: 179
Period size: 62 Copynumber: 2.4 Consensus size: 62
3853 GACGTGGCTT
* **
3863 GCCACATGTACCAAAAAGCAACATGTAGCACGCCACGTGT-ACCAAAAAGCGACATGAGGCAC
1 GCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTAACC-AAAAGCGACATGAGGCAC
* * * * *
3925 GCCACGTGTACCAAAAAGTGACATGTATCACGCCATGTGTAACCAAAAGTGACATGTGGCAT
1 GCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTAACCAAAAGCGACATGAGGCAC
* **
3987 GCCATGTGTTTCAAAAAGTGACA
1 GCCACGTGTACCAAAAAGTGACA
4010 CATGGCATGC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
62 70 0.96
63 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (62 bp):
GCCACGTGTACCAAAAAGTGACATGTAGCACGCCACGTGTAACCAAAAGCGACATGAGGCAC
Found at i:5197 original size:2 final size:2
Alignment explanation
Indices: 5190--5223 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5180 TACTATTTAG
5190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5224 ATTAGTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6275 original size:24 final size:24
Alignment explanation
Indices: 6241--6290 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
6231 TTATATTCCC
6241 ATGCATCTCAAAATAGAAATTTTT
1 ATGCATCTCAAAATAGAAATTTTT
*
6265 ATGCATGTCAAAATAGAAATTTTT
1 ATGCATCTCAAAATAGAAATTTTT
6289 AT
1 AT
6291 TATCATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (24 bp):
ATGCATCTCAAAATAGAAATTTTT
Found at i:7230 original size:39 final size:39
Alignment explanation
Indices: 7176--7254 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
7166 TGATCTATTA
*
7176 AATTGATGAATTGAAGACATTTGGGTTAGCTAAACTCAT
1 AATTGATGAATTGAAGAAATTTGGGTTAGCTAAACTCAT
7215 AATTGATGAATTGAAGAAATTTGGGTTAGCTAAACTCAT
1 AATTGATGAATTGAAGAAATTTGGGTTAGCTAAACTCAT
7254 A
1 A
7255 GTTAGGCCGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (39 bp):
AATTGATGAATTGAAGAAATTTGGGTTAGCTAAACTCAT
Found at i:7772 original size:17 final size:16
Alignment explanation
Indices: 7752--7800 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
7742 TAGCAGTCAT
7752 TTTTATTTATATTATTA
1 TTTTATTTATA-TATTA
*
7769 TTTTCTTTATATATTA
1 TTTTATTTATATATTA
*
7785 TCTTTTATATATATAT
1 --TTTTATTTATATAT
7801 ATATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 5 0.19
17 10 0.37
18 12 0.44
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATTTATATATTA
Found at i:7795 original size:2 final size:2
Alignment explanation
Indices: 7790--7821 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7780 TATTATCTTT
7790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7822 ATAAGCTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8424 original size:5 final size:5
Alignment explanation
Indices: 8411--8444 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
8401 CAATATGTCT
* *
8411 TTTTA TTTTG TTTTA TTTTG TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
8445 CTAATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:8426 original size:10 final size:10
Alignment explanation
Indices: 8411--8444 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
8401 CAATATGTCT
8411 TTTTATTTTG
1 TTTTATTTTG
8421 TTTTATTTTG
1 TTTTATTTTG
*
8431 TTTTATTTTA
1 TTTTATTTTG
8441 TTTT
1 TTTT
8445 CTAATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (10 bp):
TTTTATTTTG
Found at i:11191 original size:2 final size:2
Alignment explanation
Indices: 11184--11230 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
11174 TCCAAAGATG
* *
11184 TA TA TA TA AA T- TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11225 TA TA TA
1 TA TA TA
11231 AAAGATGTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11481 original size:64 final size:63
Alignment explanation
Indices: 11365--11534 Score: 171
Period size: 64 Copynumber: 2.7 Consensus size: 63
11355 AGATTTATAA
* * * * *
11365 ATTTATATATTTAATAAGATAAGTCTATAGATGCAGACTTATCAATACGTACACTCAGATGCAT
1 ATTTATATGTTTAAT-AGATGAGTCTATAGATGCAGACTTATCAATACGTACACTAAGAGGCAG
* * * * * *
11429 ATTTATATGTTTAATATGATGGGTCTATAGATACAAACTTATCAGCT-TGTACACTAAGGGGCAG
1 ATTTATATGTTTAATA-GATGAGTCTATAGATGCAGACTTATCA-ATACGTACACTAAGAGGCAG
* * *
11493 ATTTGTATGTTTTATAGAATGTGTCTATAGATGCAGACTTAT
1 ATTTATATGTTTAATAG-ATGAGTCTATAGATGCAGACTTAT
11535 TAGTACGTTC
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
63 2 0.02
64 84 0.97
65 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (63 bp):
ATTTATATGTTTAATAGATGAGTCTATAGATGCAGACTTATCAATACGTACACTAAGAGGCAG
Done.